The procedure looks ok, but I definitely suggest inspecting the top
and crd file directly using VMD. Most especially, be sure the bonds
are all correctly placed. Doing this every time before you start a
simulation can save you a world of headache. Since you call the
glycan "ligand," I assume it is not covalently bound to the protein.
If it should be bound, especially check that bond -- make sure there
are no extra atoms (two oxygens in a row, 5 bonds to a carbon,
etc...).
On Tue, Sep 7, 2010 at 4:51 PM, manoj singh <mks.amber.gmail.com> wrote:
> Thanks for your response!
>
> One more thing. Following is the command which I have used for creating the
> protein-carbohydrate complex in amber. I will be very thankful if you can
> look over it.
>
> ---
> tleap -s -f leaprc.ff99SB
> source leaprc.GLYCAM_06
> com = loadpdb PRA_crd1.pdb
> bond com.111.O1 com.112.C1
> bond com.112.O3 com.113.C1
> bond com.112.O6 com.114.C1
> check com
> solvateOct com TIP3PBOX 12.0
> charge com
> addions com K+ 0
> addions com Cl- 0
> saveamberparm com pra_crd1_solvated.prmtop pra_crd1_solvated.inpcrd
> ---
>
> Manoj
>
> On Tue, Sep 7, 2010 at 10:05 AM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
>
>> Your procedure looks fine, as does the mol2 file.
>>
>> You can also check the top and crd files directly in VMD. First load
>> the top as "Amber parm6". Then, into the same molecule, load the crd
>> file as "Amber restart".
>>
>>
>> On Mon, Sep 6, 2010 at 9:56 PM, manoj singh <mks.amber.gmail.com> wrote:
>> > Thanks for your reply!
>> >
>> > So here is what I did.
>> >
>> > First, I formatted the lig.pdb into its current form (attached).
>> >
>> > Then I used following commands
>> >
>> > ----
>> >
>> > tleap -s -f leaprc.GLYCAM_06
>> >
>> > com = loadpdb lig.pdb
>> >
>> > bond com.1.O1 com.2.C1
>> > bond com.2.O3 com.3.C1
>> > bond com.2.O6 com.4.C1
>> >
>> > saveamberparm com lig_tmp.top lig_tmp.crd
>> > savepdb com lig_tmp.pdb
>> >
>> > ----
>> >
>> > I then used top2mol2 command to create lig_tmp.mol2 file from top and crd
>> > files.
>> >
>> > The structure I am getting looks good, however, I yet to run the MD.
>> >
>> > I will be very thankful if you can cross-check this procedure.
>> >
>> > Manoj
>> >
>> > On Mon, Sep 6, 2010 at 12:24 PM, Lachele Foley (Lists) <
>> lf.list.gmail.com>wrote:
>> >
>> >> The structure in the pdb file you attached is:
>> >>
>> >> a-D-Manp-(1-3)-[a-D-Manp-(1-6)]-a-D-Manp-(1-)-OH
>> >>
>> >> In other words, a single alpha D mannopyranose has two others attached
>> >> at its 3 and 6 positions. If that is what you want, and I think
>> >> perhaps it is, then the structure is correct.
>> >>
>> >> To read the pdb into leap, you will need to place TER cards (in the
>> >> pdb file) between each of your residues then manually link them back
>> >> together in the proper order using the bond command within leap. When
>> >> a residue (your first one, VMA), is attached to more than one other
>> >> residue, leap is not always able to identify the attachment points for
>> >> subsequent residues. Inspection using VMD tells me that residue 2 is
>> >> attached at the three position and residue 3, at 6. You should also
>> >> terminate at the end of each chain (e.g., the 0MA), because if not,
>> >> you are essentially telling leap to bond that residue to the next one,
>> >> which is not what you want. Leap will happily do whatever you tell it
>> >> to do without regard to chemical sense (this is a good thing, but one
>> >> must respect it).
>> >>
>> >> There are further instructions for building a glycoprotein in the
>> >> AmberTools manual. The online glycoprotein builder should be
>> >> functional again in a day or two.
>> >>
>> >> :-) Lachele
>> >>
>> >>
>> >> On Mon, Sep 6, 2010 at 12:05 PM, manoj singh <mks.amber.gmail.com>
>> wrote:
>> >> > Hi,
>> >> >
>> >> > I want to simulate a protein-carbohydrate system using ff99SB and
>> GLYCAM
>> >> in
>> >> > Amber10. I am little confused over various issues with GLYCAM. First
>> is
>> >> the
>> >> > residue nomenclature.
>> >> > I want to simulate {alphaMAN-1-->6-alphaMAN-3-->1-alphaMAN}. The
>> >> structure
>> >> > of the ligand is attached with the mail. Attached is the PDB file with
>> >> > residue name, which I think is consistent with the GLYCAM. I will be
>> >> very
>> >> > thankful if someone can verify this.
>> >> >
>> >> > Manoj
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> :-) Lachele
>> >> Lachele Foley
>> >> CCRC/UGA
>> >> Athens, GA USA
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
>>
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>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Sep 08 2010 - 07:00:04 PDT
